Contacts of the strand formed by residues 160 - 166 (chain B) in PDB entry 3LUE
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 160 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B PRO* 3.2 7.6 - - - +
110B LEU* 3.4 0.2 - - - +
153B MET* 3.5 19.7 - - - -
154B ASP 3.1 11.7 - - - +
155B SER* 2.9 19.5 + - - +
159B VAL* 1.3 74.0 - - - +
161B HIS* 1.3 63.6 + - - +
162B THR* 5.3 1.1 - - + -
177B ARG* 3.3 4.2 - - - -
178B LEU* 2.7 43.9 + - + -
180B LEU 2.8 22.3 + - - -
181B ALA* 4.1 0.2 - - - +
261B LEU* 5.0 0.5 - - - +
274B ILE* 3.4 28.3 - - + +
277B THR* 6.2 0.7 - - + -
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Residues in contact with HIS 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B PRO* 1.6 39.5 - - + +
110B LEU* 2.1 39.4 + - - -
136B ILE* 4.2 21.6 - - + +
138B ALA* 4.7 0.5 - - - +
152B VAL 3.7 1.2 - - - +
153B MET* 3.5 2.6 - - - -
154B ASP* 2.9 34.1 + - + +
160B THR* 1.3 75.8 - - - +
162B THR* 1.3 64.5 + - - +
163B VAL* 3.9 14.8 + - + -
175B ILE* 3.3 22.9 - - + +
176B LEU 3.0 17.9 - - - -
177B ARG* 3.3 13.6 - - + +
277B THR* 6.0 0.7 - - - -
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Residues in contact with THR 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ILE* 4.3 4.5 - - + -
152B VAL 3.4 4.7 - - - +
153B MET* 3.6 19.3 - - + -
160B THR* 5.3 1.3 - - + -
161B HIS* 1.3 77.4 - - - +
163B VAL* 1.3 59.8 + - - +
164B PRO* 4.3 0.4 - - - -
175B ILE* 3.3 6.4 - - - -
176B LEU* 3.0 28.8 + - - +
274B ILE* 4.9 1.3 - - + +
277B THR* 3.4 25.5 + - + +
278B THR* 3.4 38.1 - - - +
281B SER* 3.0 24.5 + - - -
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Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ILE* 5.4 2.5 - - + -
138B ALA* 5.0 6.1 - - + -
139B VAL* 3.6 34.1 - - + -
151B ILE* 3.2 23.1 - - - +
152B VAL* 3.2 16.8 + - + +
161B HIS* 3.9 20.0 - - + +
162B THR* 1.3 79.1 - - - +
164B PRO* 1.3 60.6 - - - +
165B ILE* 3.8 16.4 + - + +
170B ALA* 3.8 23.6 - - + -
175B ILE* 4.0 18.6 - - + -
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Residues in contact with PRO 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B GLY 3.8 5.6 - - - +
151B ILE* 4.0 6.7 - - + -
163B VAL* 1.3 82.7 - - - +
165B ILE* 1.3 54.1 + - - +
170B ALA* 3.5 2.1 - - - -
171B LEU* 2.7 42.5 + - + +
174B ALA* 3.5 31.9 - - + +
175B ILE* 4.1 2.9 - - + +
281B SER* 3.8 14.1 - - - -
285B CYS* 3.2 37.0 - - - -
293B LEU* 3.8 13.5 - - + -
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Residues in contact with ILE 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B VAL* 5.3 5.4 - - + -
142B LEU* 1.5 66.9 - - + -
148B THR* 3.4 21.1 - - - +
149B THR* 3.2 6.9 - - - +
150B GLY 2.9 36.4 + - - +
152B VAL* 4.1 5.2 - - + -
163B VAL* 3.9 21.8 - - + +
164B PRO* 1.3 75.1 - - - +
166B TYR* 1.3 57.3 + - - +
168B GLY* 3.6 7.2 - - - +
169B TYR 3.2 22.2 - - - +
170B ALA* 3.8 15.0 - - + +
171B LEU* 4.7 0.4 - - - -
293B LEU* 4.1 4.1 - - - +
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Residues in contact with TYR 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B THR* 3.8 15.5 - - + -
165B ILE* 1.3 70.0 - - - +
167B GLU* 1.3 100.9 + - + +
169B TYR* 2.9 26.7 + + - +
171B LEU* 4.0 17.7 - - + +
289B ILE* 3.8 41.3 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il